3HTV | pdb_00003htv

Crystal structure of D-allose kinase (NP_418508.1) from ESCHERICHIA COLI K12 at 1.95 A resolution

PDB DOI: https://doi.org/10.2210/pdb3HTV/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-12 Released: 2009-06-23
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.241 (Depositor), 0.250 (DCC)
R-Value Work:
0.197 (Depositor), 0.210 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of D-allose kinase (NP_418508.1) from ESCHERICHIA COLI K12 at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 34.43 kDa
Atom Count: 2,300
Modeled Residue Count: 279
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-allose kinase	A	310	Escherichia coli K-12	Mutation(s): 0 Gene Names: alsK, b4084, JW5724, NP_418508.1, yjcT EC: 2.7.1.55
UniProt
Find proteins for P32718 (Escherichia coli (strain K12)) Explore P32718 Go to UniProtKB: P32718
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32718
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.241 (Depositor), 0.250 (DCC)
R-Value Work: 0.197 (Depositor), 0.210 (DCC)
R-Value Observed: 0.199 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33HTV

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.716	α = 90
b = 101.394	β = 90
c = 131.465	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-06-23

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-06-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references
Version 1.5: 2024-11-27
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.